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From drusch@tcag.org  Mon Dec  2 20:47:59 2002
From: drusch@tcag.org (Doug Rusch)
Date: Mon, 2 Dec 2002 15:47:59 -0500
Subject: [Biojava-dev] blast parsing slowness
Message-ID: <9A1D3672623FE64DA00A67D12BC679988BCA9A@exchange2.vfirm.com>

This is a good topic for consideration with BioJava2.

The circumstances are this: I have my blast parser working in my personal experimental biojava package. The blast data I am parsing was generated by blasting 1 mb human genomic chunks against small sequences (basically ests), so 1 query many different subjects. Anyways, I did comparisons of the java code against a home brewed perl blast parser. The biojava was much slower (at least an order of magnatitude slower) than the perl code. Now this isnt quite a fair test because the design of the two parsers is completely different but if anything I would still expect Java to be faster than perl.

I profiled the code and found that the vast majority of the processing time was being spent in org.biojava.utils.ChangeSupport.growIfNecessary. Everytime it creates an alignment (org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSubHit) it is adding a changeListener to the generic alphabet (org.biojava.bio.symbol.SimpleSymbolList.addListener) it is using for alignments. Obviously it is adding many thousands of change listeners to the alphabet, but to add insult to injury, the listeners are all ALWAYS_VETO. So this poor alphabet has thousands of listeners telling it not to change.

Is this really what was intended? I get the impression that the ALWAYS_VETO changeListener is a special case. Perhaps ALWAYS_VETO listeners should just be kept track of by a counter? Should alphabets be changable at all? I do not know what use cases prompted this design but is there any concensus on a fix?

Doug Rusch
drusch@tcag.org 





From heuermh@acm.org  Mon Dec  2 20:56:36 2002
From: heuermh@acm.org (Michael L. Heuer)
Date: Mon, 2 Dec 2002 15:56:36 -0500 (EST)
Subject: [Biojava-dev] blast parsing slowness
In-Reply-To: <9A1D3672623FE64DA00A67D12BC679988BCA9A@exchange2.vfirm.com>
Message-ID: <Pine.GSO.4.44.0212021553550.22594-100000@shell3.shore.net>

sounds like a bug to me.  At a minimum those ALWAYS_VETO listeners should
be optimized away.

I'm of the opinion that it would be better to have truely immutable
implementations of the interfaces in addition to the mutable ones with
ChangeEvent support than the current design.

What do others think?

   michael


On Mon, 2 Dec 2002, Doug Rusch wrote:

> This is a good topic for consideration with BioJava2.
>
> The circumstances are this: I have my blast parser working in my personal experimental biojava package. The blast data I am parsing was generated by blasting 1 mb human genomic chunks against small sequences (basically ests), so 1 query many different subjects. Anyways, I did comparisons of the java code against a home brewed perl blast parser. The biojava was much slower (at least an order of magnatitude slower) than the perl code. Now this isnt quite a fair test because the design of the two parsers is completely different but if anything I would still expect Java to be faster than perl.
>
> I profiled the code and found that the vast majority of the processing time was being spent in org.biojava.utils.ChangeSupport.growIfNecessary. Everytime it creates an alignment (org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSubHit) it is adding a changeListener to the generic alphabet (org.biojava.bio.symbol.SimpleSymbolList.addListener) it is using for alignments. Obviously it is adding many thousands of change listeners to the alphabet, but to add insult to injury, the listeners are all ALWAYS_VETO. So this poor alphabet has thousands of listeners telling it not to change.
>
> Is this really what was intended? I get the impression that the ALWAYS_VETO changeListener is a special case. Perhaps ALWAYS_VETO listeners should just be kept track of by a counter? Should alphabets be changable at all? I do not know what use cases prompted this design but is there any concensus on a fix?
>
> Doug Rusch
> drusch@tcag.org
>
>
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev
>


From mark.schreiber@agresearch.co.nz  Mon Dec  2 20:57:17 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 3 Dec 2002 09:57:17 +1300
Subject: [Biojava-dev] blast parsing slowness
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165011FE470@inbox.agresearch.co.nz>

Hmm, me thinks there should only be one listener. I think this should be
fixed before BJ1.3.

Following your description I wasn't able to find the exact point where
all these listeners get added. Could you give me a line number or
something?

Profiling of the common methods in general could be a good thing before
BJ1.3 and BJ2. It has helped spot things that work but do unneeded
stuff.

- Mark

> -----Original Message-----
> From: Doug Rusch [mailto:drusch@tcag.org] 
> Sent: Tuesday, 3 December 2002 9:48 a.m.
> To: biojava-dev@biojava.org
> Subject: RE: [Biojava-dev] blast parsing slowness
> 
> 
> This is a good topic for consideration with BioJava2.
> 
> The circumstances are this: I have my blast parser working in 
> my personal experimental biojava package. The blast data I am 
> parsing was generated by blasting 1 mb human genomic chunks 
> against small sequences (basically ests), so 1 query many 
> different subjects. Anyways, I did comparisons of the java 
> code against a home brewed perl blast parser. The biojava was 
> much slower (at least an order of magnatitude slower) than 
> the perl code. Now this isnt quite a fair test because the 
> design of the two parsers is completely different but if 
> anything I would still expect Java to be faster than perl.
> 
> I profiled the code and found that the vast majority of the 
> processing time was being spent in 
> org.biojava.utils.ChangeSupport.growIfNecessary. Everytime it 
> creates an alignment 
> (org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSub
> Hit) it is adding a changeListener to the generic alphabet 
> (org.biojava.bio.symbol.SimpleSymbolList.addListener) it is 
> using for alignments. Obviously it is adding many thousands 
> of change listeners to the alphabet, but to add insult to 
> injury, the listeners are all ALWAYS_VETO. So this poor 
> alphabet has thousands of listeners telling it not to change.
> 
> Is this really what was intended? I get the impression that 
> the ALWAYS_VETO changeListener is a special case. Perhaps 
> ALWAYS_VETO listeners should just be kept track of by a 
> counter? Should alphabets be changable at all? I do not know 
> what use cases prompted this design but is there any 
> concensus on a fix?
> 
> Doug Rusch
> drusch@tcag.org 
> 
> 
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-dev
> 
=======================================================================
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From matthew_pocock@yahoo.co.uk  Mon Dec  2 21:21:20 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Mon, 02 Dec 2002 21:21:20 +0000
Subject: [Biojava-dev] blast parsing slowness
In-Reply-To: <9A1D3672623FE64DA00A67D12BC679988BCA9A@exchange2.vfirm.com>
References: <9A1D3672623FE64DA00A67D12BC679988BCA9A@exchange2.vfirm.com>
Message-ID: <3DEBCED0.1010009@yahoo.co.uk>

This is a bonefidey bug. Could you send me the app & I will fix it.

Matthew

Doug Rusch wrote:
> This is a good topic for consideration with BioJava2.
> 
> The circumstances are this: I have my blast parser working in my personal experimental biojava package. The blast data I am parsing was generated by blasting 1 mb human genomic chunks against small sequences (basically ests), so 1 query many different subjects. Anyways, I did comparisons of the java code against a home brewed perl blast parser. The biojava was much slower (at least an order of magnatitude slower) than the perl code. Now this isnt quite a fair test because the design of the two parsers is completely different but if anything I would still expect Java to be faster than perl.
> 
> I profiled the code and found that the vast majority of the processing time was being spent in org.biojava.utils.ChangeSupport.growIfNecessary. Everytime it creates an alignment (org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSubHit) it is adding a changeListener to the generic alphabet (org.biojava.bio.symbol.SimpleSymbolList.addListener) it is using for alignments. Obviously it is adding many thousands of change listeners to the alphabet, but to add insult to injury, the listeners are all ALWAYS_VETO. So this poor alphabet has thousands of listeners telling it not to change.
> 
> Is this really what was intended? I get the impression that the ALWAYS_VETO changeListener is a special case. Perhaps ALWAYS_VETO listeners should just be kept track of by a counter? Should alphabets be changable at all? I do not know what use cases prompted this design but is there any concensus on a fix?
> 
> Doug Rusch
> drusch@tcag.org 
> 
> 
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev
> 


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From matthew_pocock@yahoo.co.uk  Tue Dec  3 14:37:16 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Tue, 3 Dec 2002 14:37:16 +0000 (GMT)
Subject: [Biojava-dev] sequence DB mess
Message-ID: <20021203143716.18763.qmail@web14912.mail.yahoo.com>

Hi,

We have NCBISequenceDB, WebSequenceDB, {Genbank,
Genpept, Swissprot}SequenceDB all doing similar or
overlapping things. Could we rationalize pre release?

I'm unsure which of these work, or are used. Any
ideas?

Matthew

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From mark.schreiber@agresearch.co.nz  Tue Dec  3 20:38:41 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 4 Dec 2002 09:38:41 +1300
Subject: [Biojava-dev] sequence DB mess
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165011FE5D7@inbox.agresearch.co.nz>

I recently made WebSequenceDB and NCBISequenceDB to work. The fact that
it didn't previously probably means no one was using it. I agree that
some rationalisation would be v. good.

The problem is exasperated by diverse services. For example you can
access lots of NCBI services through URLs, you can also do it through
the Qblast service (which does entrez stuff as well). Qblast is
potentially much more powerful than the URL service and Qblast can also
be set up in house.

Is there a nice model from bioperl we can steal? Might this be a case
for webservices?

- Mark


> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Wednesday, 4 December 2002 3:37 a.m.
> To: biojava-dev@biojava.org
> Subject: [Biojava-dev] sequence DB mess
> 
> 
> Hi,
> 
> We have NCBISequenceDB, WebSequenceDB, {Genbank,
> Genpept, Swissprot}SequenceDB all doing similar or
> overlapping things. Could we rationalize pre release?
> 
> I'm unsure which of these work, or are used. Any
> ideas?
> 
> Matthew
> 
> __________________________________________________
> Do You Yahoo!?
> Everything you'll ever need on one web page
> from News and Sport to Email and Music Charts 
> http://uk.my.yahoo.com >
_______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-dev
> 
=======================================================================
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From matthew_pocock@yahoo.co.uk  Wed Dec  4 23:17:54 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Wed, 04 Dec 2002 23:17:54 +0000
Subject: [Biojava-dev] blast parsing slowness
In-Reply-To: <9A1D3672623FE64DA00A67D12BC679988BCA9A@exchange2.vfirm.com>
References: <9A1D3672623FE64DA00A67D12BC679988BCA9A@exchange2.vfirm.com>
Message-ID: <3DEE8D22.8050009@yahoo.co.uk>

Doug,

Could you try again now? Thomas has committed a fix to the event 
meta-data. We'd kind of mucked some of the plumbing up.

Matthew

Doug Rusch wrote:
> This is a good topic for consideration with BioJava2.
> 
> The circumstances are this: I have my blast parser working in my personal experimental biojava package. The blast data I am parsing was generated by blasting 1 mb human genomic chunks against small sequences (basically ests), so 1 query many different subjects. Anyways, I did comparisons of the java code against a home brewed perl blast parser. The biojava was much slower (at least an order of magnatitude slower) than the perl code. Now this isnt quite a fair test because the design of the two parsers is completely different but if anything I would still expect Java to be faster than perl.
> 
> I profiled the code and found that the vast majority of the processing time was being spent in org.biojava.utils.ChangeSupport.growIfNecessary. Everytime it creates an alignment (org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSubHit) it is adding a changeListener to the generic alphabet (org.biojava.bio.symbol.SimpleSymbolList.addListener) it is using for alignments. Obviously it is adding many thousands of change listeners to the alphabet, but to add insult to injury, the listeners are all ALWAYS_VETO. So this poor alphabet has thousands of listeners telling it not to change.
> 
> Is this really what was intended? I get the impression that the ALWAYS_VETO changeListener is a special case. Perhaps ALWAYS_VETO listeners should just be kept track of by a counter? Should alphabets be changable at all? I do not know what use cases prompted this design but is there any concensus on a fix?
> 
> Doug Rusch
> drusch@tcag.org 
> 
> 
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev
> 


-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

__________________________________________________
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From drusch@tcag.org  Fri Dec  6 21:20:38 2002
From: drusch@tcag.org (Doug Rusch)
Date: Fri, 6 Dec 2002 16:20:38 -0500
Subject: [Biojava-dev] blast parsing slowness
Message-ID: <9A1D3672623FE64DA00A67D12BC679988BCAC4@exchange2.vfirm.com>

So I have tested the fix and it seems good. Now the parsing is much faster and most of the time is spent handling the regex's.

Thanks alot!
Doug

-----Original Message-----
From:	Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk]
Sent:	Wed 12/4/02 6:17 PM
To:	Doug Rusch
Cc:	biojava-dev@biojava.org
Subject:	Re: [Biojava-dev] blast parsing slowness
Doug,

Could you try again now? Thomas has committed a fix to the event 
meta-data. We'd kind of mucked some of the plumbing up.

Matthew

Doug Rusch wrote:
> This is a good topic for consideration with BioJava2.
> 
> The circumstances are this: I have my blast parser working in my personal experimental biojava package. The blast data I am parsing was generated by blasting 1 mb human genomic chunks against small sequences (basically ests), so 1 query many different subjects. Anyways, I did comparisons of the java code against a home brewed perl blast parser. The biojava was much slower (at least an order of magnatitude slower) than the perl code. Now this isnt quite a fair test because the design of the two parsers is completely different but if anything I would still expect Java to be faster than perl.
> 
> I profiled the code and found that the vast majority of the processing time was being spent in org.biojava.utils.ChangeSupport.growIfNecessary. Everytime it creates an alignment (org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSubHit) it is adding a changeListener to the generic alphabet (org.biojava.bio.symbol.SimpleSymbolList.addListener) it is using for alignments. Obviously it is adding many thousands of change listeners to the alphabet, but to add insult to injury, the listeners are all ALWAYS_VETO. So this poor alphabet has thousands of listeners telling it not to change.
> 
> Is this really what was intended? I get the impression that the ALWAYS_VETO changeListener is a special case. Perhaps ALWAYS_VETO listeners should just be kept track of by a counter? Should alphabets be changable at all? I do not know what use cases prompted this design but is there any concensus on a fix?
> 
> Doug Rusch
> drusch@tcag.org 
> 
> 
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev
> 


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From mark.schreiber@agresearch.co.nz  Sun Dec  8 22:59:01 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Mon, 9 Dec 2002 11:59:01 +1300
Subject: [Biojava-dev] Suggestion for Canonical Symbols
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165011FEAE0@inbox.agresearch.co.nz>

Hi -

If you translate and RNA SymbolList into Protein the Symbols in the
protein SymbolList come from the alphabet referenced by the
ProteinTools.getTAlphabet.

The Symbols from the Talphabet are not canonical with the Symbols from
the other protein Alphabet. This has lead to some very surprising bugs
in some stuff we were developing. Given that Integer Symbols are now
canonical even if they come from IntegerAlphabet or one of the
Integer.SubAlphabets could the same happen for the protein Alphabets?

Thanks

Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
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material. Any review, retransmission, dissemination or other use of, or
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From td2@sanger.ac.uk  Mon Dec  9 00:00:20 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Mon, 9 Dec 2002 00:00:20 +0000
Subject: [Biojava-dev] Suggestion for Canonical Symbols
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165011FEAE0@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165011FEAE0@inbox.agresearch.co.nz>
Message-ID: <20021209000020.GB162243@jabba.sanger.ac.uk>

On Mon, Dec 09, 2002 at 11:59:01AM +1300, Schreiber, Mark wrote:
> Hi -
> 
> If you translate and RNA SymbolList into Protein the Symbols in the
> protein SymbolList come from the alphabet referenced by the
> ProteinTools.getTAlphabet.
> 
> The Symbols from the Talphabet are not canonical with the Symbols from
> the other protein Alphabet. This has lead to some very surprising bugs
> in some stuff we were developing. Given that Integer Symbols are now
> canonical even if they come from IntegerAlphabet or one of the
> Integer.SubAlphabets could the same happen for the protein Alphabets?

*sigh*

That was actually the original behaviour.  I broke it
(deliberately) a few weeks ago when fixing the knotty 
question of serializing ambiguous symbols, so now you know
who to blame.  At the time, requiring that all well-known
symbols should be scoped by Alphabet provided a sane way
of cleaning up the serialization code without having to write
totally new Symbol and Alphabet implementations for all the
well-known cases.  At least in the Protein/protein-term
case is probably does make sense to fix this.  I shall
ponder -- all suggestions welcome.

The division between protein and protein-term is really
rather articificial.  As far as I can tell, the termination
symbol is a bit like the gap symbol, in that it never occurs
in "biologically real" sequences, but is a useful convenience
for computation.  Maybe we'll be able to build on that idea for
BJ2 and get rid of the annoying distinction.

     Thomas.

From mark.schreiber@agresearch.co.nz  Mon Dec  9 00:08:44 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Mon, 9 Dec 2002 13:08:44 +1300
Subject: [Biojava-dev] Suggestion for Canonical Symbols
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165011FEB04@inbox.agresearch.co.nz>

Would it be useful to use the Integer/ SubInteger model where protein
alphabet is a sub alphabet of protein-term?

> -----Original Message-----
> From: Thomas Down [mailto:td2@sanger.ac.uk] 
> Sent: Monday, 9 December 2002 1:00 p.m.
> To: Schreiber, Mark
> Cc: biojava-dev@biojava.org
> Subject: Re: [Biojava-dev] Suggestion for Canonical Symbols
> 
> 
> On Mon, Dec 09, 2002 at 11:59:01AM +1300, Schreiber, Mark wrote:
> > Hi -
> > 
> > If you translate and RNA SymbolList into Protein the Symbols in the 
> > protein SymbolList come from the alphabet referenced by the 
> > ProteinTools.getTAlphabet.
> > 
> > The Symbols from the Talphabet are not canonical with the 
> Symbols from 
> > the other protein Alphabet. This has lead to some very 
> surprising bugs 
> > in some stuff we were developing. Given that Integer 
> Symbols are now 
> > canonical even if they come from IntegerAlphabet or one of the 
> > Integer.SubAlphabets could the same happen for the protein 
> Alphabets?
> 
> *sigh*
> 
> That was actually the original behaviour.  I broke it
> (deliberately) a few weeks ago when fixing the knotty 
> question of serializing ambiguous symbols, so now you know
> who to blame.  At the time, requiring that all well-known 
> symbols should be scoped by Alphabet provided a sane way of 
> cleaning up the serialization code without having to write 
> totally new Symbol and Alphabet implementations for all the 
> well-known cases.  At least in the Protein/protein-term case 
> is probably does make sense to fix this.  I shall ponder -- 
> all suggestions welcome.
> 
> The division between protein and protein-term is really
> rather articificial.  As far as I can tell, the termination 
> symbol is a bit like the gap symbol, in that it never occurs 
> in "biologically real" sequences, but is a useful convenience 
> for computation.  Maybe we'll be able to build on that idea 
> for BJ2 and get rid of the annoying distinction.
> 
>      Thomas.
> 
=======================================================================
Attention: The information contained in this message and/or attachments
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to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
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From td2@sanger.ac.uk  Mon Dec  9 01:02:34 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Mon, 9 Dec 2002 01:02:34 +0000
Subject: [Biojava-dev] Suggestion for Canonical Symbols
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165011FEB04@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165011FEB04@inbox.agresearch.co.nz>
Message-ID: <20021209010234.GC162243@jabba.sanger.ac.uk>

On Mon, Dec 09, 2002 at 01:08:44PM +1300, Schreiber, Mark wrote:
> Would it be useful to use the Integer/ SubInteger model where protein
> alphabet is a sub alphabet of protein-term?

That's certainly a possibility.  The problem comes with sorting
out the SymbolTokenizations.  Currently, the Protein-TERM
tokenization has an "X" symbol which includes all possibly
symbols _including TER_, which is different from the "X"
in PROTEIN.  Now, I don't know if this is important to anyone.
In fact, personally I can't help wondering if it's wrong.
On the other hand, thr translation of the coding "nnn" does
include our hypothetical termination symbol.

This doesn't prevent us going the sub-alphabet route, but
it does mean we need to be careful to make sure everything
ends up with the right tokenization.

     Thomas.

From mark.schreiber@agresearch.co.nz  Tue Dec 10 03:46:43 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 10 Dec 2002 16:46:43 +1300
Subject: [Biojava-dev] Biojava in Anger
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650126CFBC@inbox.agresearch.co.nz>

Hi -

I have setup some web pages that provide a cookbook, how to, kind of
approach to performing basic tasks in biojava. It's available at
http://bioconf.otago.ac.nz/biojava/

Comments, suggestions, flames and financial support all welcome.

Enjoy

Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
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From MCCon012@mc.duke.edu  Tue Dec 10 14:36:35 2002
From: MCCon012@mc.duke.edu (Patrick McConnell)
Date: Tue, 10 Dec 2002 09:36:35 -0500
Subject: [Biojava-dev] Re: [Biojava-l] Biojava in Anger
Message-ID: <OF006A8A54.35934974-ON85256C8B.00501616-85256C8B.0050758D@notes.duke.edu>

I think this is great!

The more stuff like this that BioJava has, the better.  These are the sorts
of things that I think really help a software library become more usable.

-Patrick





"Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
12/09/2002 10:46:43 PM

Sent by:    biojava-l-admin@biojava.org


To:    <BIOJAVA-L@biojava.org>, <biojava-dev@biojava.org>
cc:

Subject:    [Biojava-l] Biojava in Anger

Hi -

I have setup some web pages that provide a cookbook, how to, kind of
approach to performing basic tasks in biojava. It's available at
http://bioconf.otago.ac.nz/biojava/

Comments, suggestions, flames and financial support all welcome.

Enjoy

Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
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From mark.schreiber@agresearch.co.nz  Thu Dec 12 22:07:32 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Fri, 13 Dec 2002 11:07:32 +1300
Subject: [Biojava-dev] Blast version support
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650126D331@inbox.agresearch.co.nz>

Hi -

The setModeLazy() argument doesn't seem to allow the use of blastn files
with unsupported version numbers. Is this method working?

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
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sender immediately.
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From mark.schreiber@agresearch.co.nz  Thu Dec 12 22:42:38 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Fri, 13 Dec 2002 11:42:38 +1300
Subject: [Biojava-dev] Java 1.4 code in cvs
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650126D354@inbox.agresearch.co.nz>

Hi -

The IndexedAnnotationDB class contains references to XMLEncoder and
XMLDecoder. These are only in jdk 1.4. Is there a work around or do we
need to bite the bullet and go to java 1.4 for biojava 1.3?

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
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From matthew_pocock@yahoo.co.uk  Fri Dec 13 00:09:34 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Fri, 13 Dec 2002 00:09:34 +0000 (GMT)
Subject: [Biojava-dev] Java 1.4 code in cvs
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE51650126D354@inbox.agresearch.co.nz>
Message-ID: <20021213000934.42146.qmail@web14912.mail.yahoo.com>

Sorry. My Bad. I'll move it to the src-1.4 dir. A lot
of the parsing stuff I'm writing uses 1.4 features,
and xml-serialization is much better than .ser files.

Matthew

 --- "Schreiber, Mark"
<mark.schreiber@agresearch.co.nz> wrote: > Hi -
> 
> The IndexedAnnotationDB class contains references to
> XMLEncoder and
> XMLDecoder. These are only in jdk 1.4. Is there a
> work around or do we
> need to bite the bullet and go to java 1.4 for
> biojava 1.3?
> 
> - Mark
> 
> 
> Mark Schreiber PhD
> Bioinformatics
> AgResearch Invermay
> PO Box 50034
> Mosgiel
> New Zealand
>  
> PH:   +64 3 489 9175
> FAX:  +64 3 489 3739
> 
>
=======================================================================
> Attention: The information contained in this message
> and/or attachments
> from AgResearch Limited is intended only for the
> persons or entities
> to which it is addressed and may contain
> confidential and/or privileged
> material. Any review, retransmission, dissemination
> or other use of, or
> taking of any action in reliance upon, this
> information by persons or
> entities other than the intended recipients is
> prohibited by AgResearch
> Limited. If you have received this message in error,
> please notify the
> sender immediately.
>
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> 
> _______________________________________________
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From francois.pepin@mail.mcgill.ca  Fri Dec 13 02:05:31 2002
From: francois.pepin@mail.mcgill.ca (Francois Pepin)
Date: Thu, 12 Dec 2002 21:05:31 -0500
Subject: [Biojava-dev] FW: Suffix tree
Message-ID: <000301c2a24c$1df25470$94a72581@hermes>

Hi everyone,

Is there anyone planning on doing a new version of the SuffixTree? Is
there a reason I shouldn't go and do it myself?

I've got a pretty good implementation of Ukkonen's suffix tree algorithm
that I shouldn't need to modify all that much to fit the current
methods, and it should make it a lot faster for the tree creation
(O(n)). It's also got a lot more features than the current one (since I
needed it to do some ).

Or would it be better to just have it subclass it and override
everything and then people can see what it's worth?

François Pepin



From matthew_pocock@yahoo.co.uk  Fri Dec 13 10:10:24 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Fri, 13 Dec 2002 10:10:24 +0000 (GMT)
Subject: [Biojava-dev] FW: Suffix tree
In-Reply-To: <000301c2a24c$1df25470$94a72581@hermes>
Message-ID: <20021213101025.75299.qmail@web14905.mail.yahoo.com>

Hi François,

The suffix tree impl is my fault. I wrote it as a
quick-and-dirty way to do kernel methods (like support
vector machines) over sequences. Since you have
working code, the best plan is probably for you to add
it to biojava as a seperate class, and then we can
work out how to provide both implementations to people
without twice the API.

Have you replaced SuffixTree with your code, or is it
a totaly seperate implementation?

Anyway, send code and get added to the biojava 1.3
authors list.

Matthew

 --- Francois Pepin <francois.pepin@mail.mcgill.ca>
wrote: > Hi everyone,
> 
> Is there anyone planning on doing a new version of
> the SuffixTree? Is
> there a reason I shouldn't go and do it myself?
> 
> I've got a pretty good implementation of Ukkonen's
> suffix tree algorithm
> that I shouldn't need to modify all that much to fit
> the current
> methods, and it should make it a lot faster for the
> tree creation
> (O(n)). It's also got a lot more features than the
> current one (since I
> needed it to do some ).
> 
> Or would it be better to just have it subclass it
> and override
> everything and then people can see what it's worth?
> 
> François Pepin
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev 

__________________________________________________
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From td2@sanger.ac.uk  Sat Dec 14 20:06:18 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Sat, 14 Dec 2002 20:06:18 +0000
Subject: [Biojava-dev] Suggestion for Canonical Symbols
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165011FEAE0@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165011FEAE0@inbox.agresearch.co.nz>
Message-ID: <20021214200618.GA209830@jabba.sanger.ac.uk>

On Mon, Dec 09, 2002 at 11:59:01AM +1300, Schreiber, Mark wrote:
> Hi -
> 
> If you translate and RNA SymbolList into Protein the Symbols in the
> protein SymbolList come from the alphabet referenced by the
> ProteinTools.getTAlphabet.

Okay, I've fixed this one now -- we're back to the tried and
tested system of allowing the well-known symbols to be global,
rather than always scoped by alphabet.  The code has been refactored
a lot now, so I was able to find an alternative way round getting
ambiguity symbol serialization to work.

The tests still pass, and a few programs I've tried seem to be
okay, but more testing in anger would be good.

    Thomas.


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From smh1008@cus.cam.ac.uk  Mon Dec 16 10:30:24 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Mon, 16 Dec 2002 10:30:24 +0000
Subject: [Biojava-dev] SAX use conventions
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165011FEB04@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165011FEB04@inbox.agresearch.co.nz>
Message-ID: <200212161030.25122.smh1008@cus.cam.ac.uk>

While debugging a problem with the use of the blast XML parser with 
BlastLikeSearchBuilder, I have come against a problem that may be best 
solved by us deciding on and sticking to a convention when using SAX.

When I wrote the blast XML parser, SAX was called with both the local and 
fully qualified names of elements/attributes in the parameter list.  This 
is incompatible with the use of SAX within BlastLikeSearchBuilder where 
attributes are recovered by calling the version of the getAttribute method 
that expects a XML 1.0 qualified name with the local name.  Nothing ever 
gets returned as a result.

I can fix this in one of two ways:-
i) change the blast xml parser to write out local names only to attributes
OR
ii) change ssbind to use the getAttributes call that expects the namespace 
URI and local name.  If this is done, will it break anything else?

Are there any views as to which solution is preferred?  I would probably 
prefer (ii) but I'd rather canvass opinion to establish a convention we can 
stick to hereafter.

Regards,
David Huen



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From: glorja_kovac@latinmail.com (glorja kovac)
Date: Mon, 16 Dec 2002 08:20:50 -0500
Subject: [Biojava-dev] CAN YOU ASSIST ME?
Message-ID: <20021216132046.2F1D93BE5E@smtp.latinmail.com>

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From drusch@tcag.org  Mon Dec 30 03:15:11 2002
From: drusch@tcag.org (Doug Rusch)
Date: Sun, 29 Dec 2002 22:15:11 -0500
Subject: [Biojava-dev] paired feature problem
Message-ID: <9A1D3672623FE64DA00A67D12BC679988BCB42@exchange2.vfirm.com>

Is there a bug with the SimilarityPairBuilder in ssbind?

I am trying to instantiate the paired features, this is going fine, except that the sibling is coming back as null. Now I have been looking at how the templates  are used to create these features. There is no way for the templates to know what their sibling feaure will be given that the sib hasnt been created yet much less assigned to the template.

What was the plan for this when the PairedFeature was first created?

Happy Holidays everyone :)

Doug Rusch
TCAG.org


From kdj@sanger.ac.uk  Mon Dec 30 21:30:15 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 30 Dec 2002 21:30:15 +0000
Subject: [Biojava-dev] paired feature problem
In-Reply-To: <9A1D3672623FE64DA00A67D12BC679988BCB42@exchange2.vfirm.com>
References: <9A1D3672623FE64DA00A67D12BC679988BCB42@exchange2.vfirm.com>
Message-ID: <sc4wulrfb4o.fsf@adnah.sanger.ac.uk>

>>>>> "Doug" == Doug Rusch <drusch@tcag.org> writes:

    Doug> Is there a bug with the SimilarityPairBuilder in ssbind?  I
    Doug> am trying to instantiate the paired features, this is going
    Doug> fine, except that the sibling is coming back as null. Now I
    Doug> have been looking at how the templates are used to create
    Doug> these features. There is no way for the templates to know
    Doug> what their sibling feaure will be given that the sib hasnt
    Doug> been created yet much less assigned to the template.

You're right in all respects. Serves me right for not following my own
advice and including a test. I've added a setSibling method but
retained the sibling field in the template (for use in creating new
templates from an existing feature which has its sibling correctly
set) and fixed a less obvious defect in the features (I hadn't
overridden the superclass getTemplate). Updated the builder (will add
test after vacation).

There's a unit test for the feature too. Sorry for the inconvenience.

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -


From perf-remove.4981.139095.12504924.0.0.1@b.list-email.net  Tue Dec 31 02:01:59 2002
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Date: Mon, 30 Dec 2002 18:01:59 -0800
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